Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Mapping population”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 991 records · Page 55Linked to original sources

Remapping of neural activity in the motor colliculus: a neural network study.

Neurophysiological studies have shown that the deeper layers of the superior colliculus (SC) contain a topographical neural map representing the ocular vectorial displacement required for foveation of the target (motor error). It is known that the location of the active area in this neural map can be updated, not only following changes in retinal error, but also by efference-copy signals representing a change in eye position. Since it can be shown that a two-layer feedforward network cannot perform this task, we have simulated this system by training a three-layered neural network with access to retinal error and efference copy information about eye position. The network was taught to code motor error topographically (as in the collicular motor map) by generating population activity at the appropriate location in its output layer for different combinations of visual and efference copy signals. After the network had learned the required remapping transformation with sufficient precision (error of one deg over an 80 x 80 deg working range), the properties of the trained network were analyzed. From an investigation of the activity patterns of the hidden units in the trained network it appeared that information about target location relative to the head, implicitly present at the level of input signals, is no longer available at the level of the hidden layer. More detailed inspection of the properties of these units revealed that they code motor error. Their movement field is a monotonic function of motor error amplitude, and shows broad direction tuning specific for each unit. Finally, simulations were made with a four layered network with an architecture and access to input signals closely mimicking Robinson's model of the saccadic system. Again, the network was trained to represent motor error topographically in its output layer. The model shows, for the first time, how the computation of the topographical motor error map in the SC from retinal and eye position signals may proceed in two steps, involving a stage where target location is coded in a distributed fashion in craniotopic coordinates and a subsequent supracollicular stage, where radial motor error is represented in a firing-rate code in units with broad tuning characteristics. These two stages in the model show interesting similarities with the characteristics of neuron populations shown neurophysiologically in area 7a and parietal region LIP, respectively.

Brain Mapping↗

[Genogeographic analysis of subdivided population. The Adyge gene pool in the Caucasian gene pool system].

A gene geographic analysis of the indigenous population of the Caucasian historical cultural province was carried out with a set of genetic markers extensively studied in the Adyges (39 alleles of 18 loci): AB0, ACP, C3, FY, GC, GLO, HP, KEL, LEW, MN, MNS, P, PGD, PGM1, RH-C, RH-D, RH-E, and TF. Genetic information on 160 Caucasian populations was used (on average, 65 populations per locus). A synthetic map of the first principal component clearly showed a division into two gene geographic provinces: Northern Caucasus and Transcaucasia. The component significantly differed across the Greater Caucasian Ridge. One of the major regions of extreme values corresponded to the Adyge region. A map of the second component revealed two poles, Northwestern (the Adyges) and Caspian, in gene pool variation of the Caucasian population. The analysis of the maps and the space of principal components showed that the Adyge population is an important component of the Caucasian gene pool. A map of genetic distance from all Caucasian populations to the Adyges showed that the north Caucasian populations (excluding the Ossetes) are the most genetically similar to the Adyges, while Georgians from the Kolkhida Valley and Azerbaijanians from the lowlands near the Caspian Sea and highland steppes are the most genetically remote from the Adyges. The genetic diversity (GST x 10(2)) of the entire Caucasian gene pool was studied. The average diversity of subpopulation within a Caucasian ethnos was GS-E = 0.81, the diversity of ethnoses within a linguistic family was GE-L = 0.83, and the diversity of linguistic families was GL-T = 0.58. The race classification of the Caucasian populations (GS-E = 0.81, GS-R = 0.80, GR-T = 0.76) proved to be more genetically informative than the linguistic one. The major parameters of the Adyges (total diversity HT = 0.364, heterozygosity HS = 0.361, and subpopulation diversity within the ethnos GS-E = 0.69) were similar to those averaged over the entire Caucasian population. A comparison with the same set of genetic markers showed that the interethnic diversity in the Caucasian region was lower than in the other north Eurasian regions (GS-E was 1.24 in the European region, 1.42 in the Ural region, 1.27 in Middle Asia, and 3.85 in Siberia).

Gene Pool↗

Quantitative trait loci affecting fertility and calving traits in Swedish dairy cattle.

Impaired fertility is the main reason for involuntary culling of dairy cows in Sweden. The objective of this study was to map quantitative trait loci (QTL) influencing fertility and calving traits in the Swedish dairy cattle population. The traits analyzed were number of inseminations, 56-d nonreturn rate, interval from calving to first insemination, fertility treatments, heat intensity score, stillbirth, and calving performance. A genome scan covering 20 bovine chromosomes was performed using 145 microsatellite markers. The mapping population consisted of 10 sires and their 417 sons in a granddaughter design. Nine of the sires were of the Swedish Red Breed, and one was a Swedish Holstein. Least squares regression was used to map loci affecting the analyzed traits, and permutation tests were used to set significance thresholds. Cofactors were used in the analyses of individual chromosomes to adjust for QTL found on other chromosomes. The use of cofactors increased both the number of QTL found and the significance level. In the initial analysis, we found 13 suggestive QTL that were mapped to chromosomes 6, 7, 9, 11, 13, 15, 20, and 29. When cofactors were included, 30 QTL were detected on chromosomes 1, 3, 4, 18, 19, 22, and 25, in addition to the 8 previously mentioned chromosomes. Some of the results from the cofactor analysis may be false positives and require further validation. In conclusion, we were able to map several QTL affecting fertility and calving traits in Swedish dairy cattle.

Animals↗

Topographic mapping from the retina to the midbrain is controlled by relative but not absolute levels of EphA receptor signaling.

Topographic maps are a fundamental feature of sensory representations in nervous systems. The formation of one such map, defined by the connection of ganglion cells in the retina to their targets in the superior colliculus of the midbrain, is thought to depend upon an interaction between complementary gradients of retinal EphA receptors and collicular ephrin-A ligands. We have tested this hypothesis by using gene targeting to elevate EphA receptor expression in a subset of mouse ganglion cells, thereby producing two intermingled ganglion cell populations that express distinct EphA receptor gradients. We find that these two populations form separate maps in the colliculus, which can be predicted as a function of the net EphA receptor level that a given ganglion cell expresses relative to its neighbors.

Animals↗

A general pipeline for the development of anchor markers for comparative genomics in plants.

BACKGROUND: Complete or near-complete genomic sequence information is presently only available for a few plant species representing a large phylogenetic diversity among plants. In order to effectively transfer this information to species lacking sequence information, comparative genomic tools need to be developed. Molecular markers permitting cross-species mapping along co-linear genomic regions are central to comparative genomics. These "anchor" markers, defining unique loci in genetic linkage maps of multiple species, are gene-based and possess a number of features that make them relatively sparse. To identify potential anchor marker sequences more efficiently, we have established an automated bioinformatic pipeline that combines multi-species Expressed Sequence Tags (EST) and genome sequence data. RESULTS: Taking advantage of sequence data from related species, the pipeline identifies evolutionarily conserved sequences that are likely to define unique orthologous loci in most species of the same phylogenetic clade. The key features are the identification of evolutionarily conserved sequences followed by automated design of intron-flanking Polymerase Chain Reaction (PCR) primer pairs. Polymorphisms can subsequently be identified by size- or sequence variation of PCR products, amplified from mapping parents or populations. We illustrate our procedure in legumes and grasses and exemplify its application in legumes, where model plant studies and the genome- and EST-sequence data available have a potential impact on the breeding of crop species and on our understanding of the evolution of this large and diverse family. CONCLUSION: We provide a database of 459 candidate anchor loci which have the potential to serve as map anchors in more than 18,000 legume species, a number of which are of agricultural importance. For grasses, the database contains 1335 candidate anchor loci. Based on this database, we have evaluated 76 candidate anchor loci with respect to marker development in legume species with no sequence information available, demonstrating the validity of this approach.

Arachis↗

Linkage disequilibrium mapping of quantitative trait loci under truncation selection.

As a dense map of single nucleotide polymorphism (SNP) markers are available, population-based linkage disequilibrium (LD) mapping or association study is becoming one of the major tools for identifying quantitative trait loci (QTL) and for fine gene mapping. However, in many cases, LD between the marker and trait locus is not very strong. Approaches that maximize the potential of detecting LD will be essential for the success of LD mapping of QTL. In this paper, we propose two strategies for increasing the probability of detecting LD: (1) phenotypic selection and (2) haplotype LD mapping. To provide the foundations for LD mapping of QTL under selection, we develop analytic tools for assessing the impact of phenotypic selection on allele and haplotype frequencies, and LD under three trait models: single trait locus, two unlinked trait loci, and two linked trait loci with or without epistasis. In addition to a traditional chi(2) test, which compares the difference in allele or haplotype frequencies in the selected sample and population sample, we present multiple regression methods for LD mapping of QTL, and investigate which methods are effective in employing phenotypic selection for QTL mapping. We also develop a statistical framework for investigating and comparing the power of the single marker and multilocus haplotype test for LD mapping of QTL. Finally, the proposed methods are applied to mapping QTL influencing variation in systolic blood pressure in an isolated Chinese population.

Chi-Square Distribution↗

Cross-ethnic group comparisons of HLA class II alleles and insulin dependent diabetes mellitus.

HLA class II associations with IDDM in populations of non-Caucasoid origin can provide important insights into the nature of the HLA and disease association. Firstly, HLA class II alleles that are rare in Caucasoids but common in other populations can be assessed for their contributory role in IDDM. Secondly, the different HLA class II gene linkage arrangements in different populations can help map the IDDM susceptibility determinants. This chapter reviews studies of HLA class II associations with IDDM in Asian Indians, Chinese, Japanese, Africans and black Americans. Most of these studies have been based on HLA-DR serology. However, DNA analyses, based on restriction fragment length polymorphism, sequence specific oligonucleotide hybridizations of polymerase chain reaction products and DNA sequencing, have made clear the identity of genes contributing to susceptibility or resistance to IDDM in populations of non-Caucasoid origin. DNA sequence analysis of the variable regions of the HLA-DQA, DQB and DRB genes has revealed at least eight alleles at HLA-DQA, 13 at HLA-DQB and 34 at HLA-DRB1. This chapter correlates HLA-DR and DQ allelic diversity with inherited predisposition to IDDM on a global basis. IDDM is strongly associated with the serological specificities of HLA-DQ, rather than with particular amino acid substitutions in class II alleles. DQw8 has a high risk for IDDM, DQw4, DQw5 and DQw9 have a lesser risk, while DQw6 and DQw7 are protective in IDDM. DQw2 is permissive for IDDM, depending on the presence of other HLA class II alleles. Increased heterozygosity at HLA is observed in Oriental patients, as it is in Caucasoid IDDM patients. The nature of this synergism is examined in terms of possible interactive effects between DQA and DQB alleles or DRB and DQB alleles; both effects could be operating. The conclusion from this genetic analysis is that molecular mimicry at HLA-DQ, with either foreign or autoantigens, may be an important mechanism in IDDM. Additionally, the anomalous role of DQw2 in IDDM suggests that a further mechanism, such as T cell activation, may control the ability to mount an immune response against autoantigens. Further studies, possibly with transfectant cell lines, are necessary to clarify the functional role of HLA class II genes in IDDM.

Alleles↗

Fos, nociception and the dorsal horn.

The protooncogene c-fos is rapidly activated after noxious stimuli to express the protein Fos in spinal dorsal horn neurons that are in the 'correct' locations for nociceptive information transfer. As such, therefore, mapping Fos expression in these neurons is at present the best global marker for efficiently locating populations of neurons in the awake animal that respond to nociceptive input. This allows, among other things, precise behavioral measurements to be correlated with Fos expression. Two arenas where mapping dorsal horn Fos expression has made a major impact are in the anatomy of nociceptive systems and as a useful assay for the analgesic properties of various therapeutic regimens. Also Fos expression is the only way to map populations of neurons that are responding to non-localized input such as withdrawal after addiction and vascular occlusion. Another insight is that it shows a clear activation of neurons in superficial 'pain-processing' laminae by innocuous stimuli after nerve lesions, a finding that presumably bears on the allodynia that often accompanies these lesions. It is to be understood, however, that the Fos localizations are not sufficient unto themselves, but the major function of these studies is to efficiently locate populations of cells in nociceptive pathways so that powerful anatomic and physiologic techniques can be brought to bear efficiently. Thus, the purpose of this review is to summarize the studies whose numbers are geometrically expanding that deal with Fos in the dorsal horn and the conclusions therefrom.

Animals↗

Mapping mortality and morbidity patterns: an international comparison.

A set of 49 national, intranational and international health atlases was surveyed to characterize their mapping methodology with respect to the populations covered, the diseases represented, the mapping techniques, and statistical methods. Little consistency was found concerning the choice of data function to be mapped, minimum event frequency requirements, method of age standardization, or map colour systems. Many atlases did not include basic epidemiological information; for instance, approximately half the atlases did not quote population denominators. There was a tendency to emphasize statistical significance over rate values, and to focus on high rather than low risk. Very few atlases included supplemental information on environmental factors. Most adopted a descriptive stance, and attempted no aetiological interpretation. We conclude that inter-atlas comparisons are made very difficult by methodological differences, and that even regional comparisons within atlases should be made cautiously. We propose a set of methodological guidelines for consideration in future atlases.

Epidemiology↗

Radioguided localisation of non-palpable breast lesions and simultaneous sentinel lymph node mapping.

The authors report their experience with a new strategy for radioguided breast surgery that combines radioguided occult lesion localisation (ROLL) and sentinel lymph node (SLN) mapping. The study population comprised 38 women with non-palpable breast lesions suspicious for breast cancer (BI-RADS 4-5). On the day before surgery, 0.2 ml solution containing particles of dextran labelled with approximately 15 MBq of technetium-99m was injected under stereotaxic guidance by mammography. All patients underwent open surgical biopsy guided by gamma probe, radiographic control of the surgical specimen and frozen section analysis. The rate of confirmation of lesion removal was 100% and the rate of simultaneous SLN mapping was 97.3% (37/38). Eleven cases of infiltrating carcinoma and eight of ductal carcinoma in situ (DCIS) were diagnosed intraoperatively. In the first eight invasive lesions, the SLN was biopsied and complete axillary lymph node dissection was performed; in the three other invasive lesions and in two aggressive cases of DCIS, only the SLN was dissected. The intraoperative results of SLN analysis and the definitive histopathological examinations of the SLN were always negative. It is concluded that ROLL and SLN can be employed simultaneously when dextran is used as a tracer; this technique allows frozen section diagnosis and intra-operative node analysis, and has many advantages over the conventional two-step procedure.

Adult↗

Auditing bacterial dark-gene screens for superimposed open reading frame artefacts: A multi-layer analysis of Rv2438A in Mycobacterium tuberculosis.

Essentiality and knockdown-vulnerability screens can promote spurious bacterial open reading frames when those frames overlap essential genes, because such a frame inherits its neighbour's signals undiluted and therefore satisfies the screen's criteria better than a genuine small gene. We present a multi-layer audit that tests this failure mode across genome annotation, transposon mutagenesis, CRISPR interference, homology, transcript mapping, proteomics, and population variation. We apply it to Rv2438A, a 92-codon conserved hypothetical open reading frame of Mycobacterium tuberculosis ranked first by our own dark-gene target screen. Rv2438A is superimposed on the essential NAD synthetase locus nadE: 44% lies within its coding sequence on the opposite strand, and the remainder covers its promoter and transcription start site. Consequently, three of five Himar1 sites lie within nadE, no CRISPRi guide can target Rv2438A without binding nadE, and the cross-species hit maps to the same nadE start junction. Rv2438A lacks its own transcription start site and is absent from every proteomic dataset that detects nadE. A genome-wide scan identifies six short, overlapping, uncharacterised loci among 3907 annotated genes, but only Rv2438A combines overlap and essentiality with non-detection across all proteomic datasets; rare genome-wide, it ranked first among screen hits. We provide an implementable audit workflow and a codon-position control, but measure the control's sensitivity as only two of five genes with attested protein, limiting it to confirmatory use. Overlap coordinates and neighbour-specific experimental resolution should therefore be reported before bacterial dark genes are prioritised.

CRISPR interference↗

Surface rendering of three-dimensional myocardial SPECT: clinical usefulness compared with bull's-eye and conventional tomograms.

BACKGROUND: A prospective study was conducted to evaluate the clinical usefulness of three-dimensional (3D) surface-shaded maps for routine practice of myocardial perfusion single-photon emission computed tomography (SPECT) by comparison with 2D slices and 2D bull's-eye qualitative analysis. METHODS AND RESULTS: Angiograms were performed on 201 consecutive patients, 155 with coronary artery disease (CAD) and 46 with no significant CAD. One-day 201TI stress/rest-reinjection protocol was performed in 110 patients, and 1-day 99mTc-sestamibi or tetrofosmin stress/rest protocol was performed in 91. The stress protocol was either exercise or dipyridamole (0.56 mg/kg) infusion. Three-dimensional surface maps were obtained by using a threshold for the transaxial data at 50%, 55%, 60%, 65%, and 70% of the maximum pixel value in the first 60 patients. Interpretation of 3D maps was based on the presence of a complete (transmural-looking) perfusion hole within the myocardial wall; doubtful patterns were considered pathologic or normal. Good diagnostic values were found for the 50% to 60% thresholds, but the 60% setting showed the best concordance with multislice and bull's-eye analysis; higher values drastically degraded the specificity. Considering doubtful patterns as normal clarified interpretation and led to a small loss in sensitivity but high gain in specificity. Applied to the whole population, the 3D maps using a 60% threshold provided similar diagnostic value to detect CAD as did conventional and bull's-eye analysis. Moreover, the 3D maps showed a trend toward higher specificity and a proportionally smaller decrease in sensitivity (sensitivity: 92.9%, 90.3%, 89.7%; specificity: 45.6%, 50.0%, 58.7% for tomograms, bull's-eye analysis, and 3D maps, respectively), especially for the detection of left anterior descending and right CAD. Multivessel disease was detected in an identical manner. Three-dimensional maps might improve detection of perfusion defects in the basal regions. However, 3D maps were found to be less sensitive than slices and particularly bull's-eye analysis for the reversibility of stress defects. CONCLUSIONS: Three-dimensional surface display of myocardial perfusion is a valuable independent tool for determining presence, extent, and location of CAD. It can convey useful first-look information to the referring physician, especially through a cine-rotational motion (as done in our practice through use of a floppy disk.

Coronary Angiography↗

Analysis of segregation distortion of molecular markers in F2 population of rice.

A genetic linkage map comprising 148 SSR markers loci was constructed using an F2 population consisting of 90 lines derived from a sub-specific cross between a japonica variety Nipponbare and an indica variety Guangluai-4. The F2 population showed high significantly distorted segregations. Among these SSR markers, 49 markers(33.11%) showed the genetics distortion(P<0.05). Of them, 36 markers deviated toward male parent indica GuangLuAi-4 and 13 markers toward heterozygote, but none toward the female parent Nipponbare. It was found that the segregation distortion might be caused by gametophyte and zygote. Since most gametophyte loci and sterility loci were mapped in segregation distortion regions, it indicated that the segregation distortion may be caused by these gametophyte loci and sterility loci. Finally, this research also analyzed the skewed segregation of some markers, which had not been mapped on chromosome.

Biomarkers↗

The use of polymorphic Alu insertions in human DNA fingerprinting.

We have characterized several Human Specific (HS) Alu insertions as either dimorphic (TPA25, PV92, APO), slightly dimorphic (C2N4 and C4N4) or monomorphic (C3N1, C4N6, C4N2, C4N5, C4N8) based on studies of Caucasian, Asian, American Black and African Black populations. Our approach is based upon: 1) PCR amplification using primers complementary to the unique DNA sequences that flank the site of insertion of the different Alu elements studied; 2) gel electrophoresis and scoring according to the presence or absence of an Alu insertion in one or both homologous chromosomes; 3) allele frequencies determined by gene counting and compared to Hardy-Weinberg expectations. Our DNA fingerprinting procedure using PCR amplification of diallelic polymorphic (dimorphic) Human Specific Alu insertions, may be used as a tool for genetic mapping, to characterize populations, study human migrational patterns, and track the inheritance of human genetic disorders.

DNA Fingerprinting↗

Isolation, characterisation and mapping of simple sequence repeat loci in potato.

Solanum tuberosum L. DNA sequences containing simple sequence repeat (SSR) motifs were extracted from the EMBL database, cDNA and selectively enriched small-insert DNA libraries. Enrichment was achieved using either triplex affinity capture or single-strand hybridisation selection. One hundred and twelve primer pairs which successfully amplified products of the correct size from potato DNA were ultimately designed and synthesised. Ninety-eight of these revealed length polymorphisms in a panel of four diploid and two tetraploid clones, in agreement with the high information content of this class of markers which has been found in other species. All of the markers were assigned a quality score of 1-5 based on their potential usefulness. Eighty-nine loci from 65 of the primer pairs were located on two genetic linkage maps of potato by segregation analysis of the amplified alleles. Fifty-two of the SSRs were clearly single locus. The maps were aligned using 23 SSR primer pairs and 13 RFLP loci mapped in both populations. The markers described constitute a class which should replace Restriction Fragment Length Polymorphisms (RFLP) as the markers of choice for future genetic studies in potato. The sequences of the primers, together with other information on these markers are provided.

Base Sequence↗

Heterozygosities of 735 microsatellite markers and background linkage disequilibrium in the Korean population.

Suitability of a specific population for linkage disequilibrium mapping studies of complex traits may be assessed by investigating the background linkage disequilibrium (BLD). We are unaware of studies for quantifying the degree of BLD in the Korean population, although the population may be a good candidate for mapping of complex trait genes through whole-genome association studies. It is useful to investigate the properties of genetic isolates in East Asia and to compare them to genetic isolates in Europe. We analyzed the extent of BLD in the Korean population using 735 microsatellite markers and compared the results with the Icelander population, which is one of the European expanded genetic isolates. The Korean population exhibited a level of BLD comparable with the Icelander population. The inference of population structure using the model with admixture showed that each individual has allele copies originating from K populations in equal proportions. Therefore, we believe that factors other than genetic distance, such as recent admixture, have not contributed to the level of BLD. Our results showed that the Korean population, which is an expanded population with no evidence of admixture, has a BLD level comparable with the Icelander population. Therefore, the Korean population can be used for fine mapping of either complex traits or monogenic diseases.

Adult↗

Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis.

The genetic architecture of transcript-level variation is largely unknown. The genetic determinants of transcript-level variation were characterized in a recombinant inbred line (RIL) population (n = 211) of Arabidopsis thaliana using whole-genome microarray analysis and expression quantitative trait loci (eQTL) mapping of transcript levels as expression traits (e-traits). Genetic control of transcription was highly complex: one-third of the quantitatively controlled transcripts/e-traits were regulated by cis-eQTL, and many trans-eQTL mapped to hotspots that regulated hundreds to thousands of e-traits. Several thousand eQTL of large phenotypic effect were detected, but almost all (93%) of the 36,871 eQTL were associated with small phenotypic effects (R(2) < 0.3). Many transcripts/e-traits were controlled by multiple eQTL with opposite allelic effects and exhibited higher heritability in the RILs than their parents, suggesting nonadditive genetic variation. To our knowledge, this is the first large-scale global eQTL study in a relatively large plant mapping population. It reveals that the genetic control of transcript level is highly variable and multifaceted and that this complexity may be a general characteristic of eukaryotes.

Arabidopsis↗

Multipoint estimation of genetic maps for human trisomies with one parent or other partial data.

Centromeric-mapping methods have been used to investigate the association between altered recombination and meiotic nondisjunction in humans. For trisomies, current methods are based on the genotypes from a trisomic offspring and both parents. Because it is sometimes difficult to obtain samples from both parents and because the ability to use sources of DNA previously not available (e.g., stored paraffin-embedded pathological samples) has increased, we have been interested in creating similar maps for trisomic populations in which one of the parents of the trisomic individual is unavailable for genotyping. In this paper, we derive multipoint likelihoods for both missing-parent data and conventional two-parent data. We find that likelihoods for two-parent data and for data generated without a sample from the correctly disjoining parent can be maximized in exactly the same way but also that missing-parent data has a high frequency of partial data of the same sort produced by intercross matings. Previously published centromeric-mapping methods use incorrect likelihoods for intercross matings and thus can perform poorly on missing-parent data. We wrote a FORTRAN program to maximize our multipoint likelihoods and used it in simulation studies to demonstrate the biases in the previous methods.

Algorithms↗